[MOBY-l] Problems starting dashboard in trunk
Ola Spjuth
ola.spjuth at farmbio.uu.se
Fri Mar 28 11:12:55 UTC 2008
Hi,
This looks exactly like my problem. Let me first say again that I am
new to maven. I could not find commons-collections in moby-live/Java/
pom.xml. I added it there like:
<dependency>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
<version>3.2</version>
</dependency>
and maven collected it for me and 3.2 now shows up in maven
dependencies of Eclipse instead of the previous 2.1, and I confirm
that map/LinkedMap is there. However, I still cannot start dashboard
(I get the same exception). Cleanall didn't help. Is there something
else I should do for the dep to be picked up by ant and build.xml?
Martin: I tried firstly from Eclipse but 'build/run/run-dashboard'
from command line gives the same exception.
Thanks,
/Ola
On Mar 28, 2008, at 11:21 , Björn Usadel wrote:
> Hi,
>
> looks very similar to what Marc experienced on his Mac.
>
> I attached his solution below. We don't know if this is the
> appropriate solution, as we are really more into Perl Biomoby than
> Java Biomoby. But this did the trick for Marc. Maybe one of the
> Java guys can chip in here?
>
> Cheers,
> Björn
> ---------------
> Hi Björn,
>
> yes i can comment on this:
>
> When looking at the stack trace of the exception thrown you see
> that it is again the
>
> java.lang.NoClassDefFoundError: org/apache/commons/collections/map/
> LinkedMap
>
> error. So you’ll need to get version 3.2 of the commons-
> collections (commons-collections-3.2.jar)
> and put it in the right place. I did this manually on the command
> line since i do know nothing about
> “maven dependencies” - but i guess that if you change “commons-
> collections-2.1.jar” to
> “commons-collections-3.2.jar” in the dependency list you’ll be fine
> after rebuilding the dashboard
> (and i suggest you do “ant clean” or whatever is the equivalent to
> this in eclipse before rebuilding).
>
> I hope this solves your problem,
>
> bests,
> Marc
>
> P.S.: I do not think this is a JVM-related problem as i am using
> the same version of
> apple’s JVM.
>
> Andreas Groscurth wrote:
>> Hi Ola,
>> I hope a apple person can jump in here because I have no idea about
>> apples and its JVM.... is it a JRE or a JDK ?
>> andreas
>> Ola Spjuth wrote:
>>> Hi Andreas,
>>>
>>> Sorry, I should have clarified this:
>>>
>>> I have apples JVM1.5.0 installed at
>>> /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0 with the
>>> following structure:
>>>
>>> Classes
>>> Commands
>>> Headers
>>> Home
>>> bin
>>> lib
>>> Libraries
>>> Resources
>>>
>>> The JRE container in Eclipse points to
>>> /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home, and
>>> setting is to not use deprecated JRE_LIB. I have set the
>>> JAVA_HOME in
>>> Eclipse and in bash to this as well, so that should not be a problem
>>> (don't know why that wasn't picked up by ant). Anyway, I can build
>>> jmoby, moses datatypes, run sample clients, but not dashboard. I do
>>> see commons-collections-2.1.jar under Maven dependencies in Eclipse.
>>>
>>> Cheers,
>>>
>>> /Ola
>>>
>>> On Mar 27, 2008, at 16:28 , Andreas Groscurth wrote:
>>>
>>>> Hi Ola,
>>>>
>>>> the current docs
>>>> (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/
>>>> EclipseAndJMoby.html)
>>>> do not suggest to edit any build files... and the 'Home' makes me
>>>> wondering - what Java installation is that ? never seen a Java
>>>> installation that has a 'Home' directory inside ?!
>>>>
>>>> which Java version do you work with - is your JAVA_HOME set
>>>> correctly
>>>> and does Eclipse uses the correct JDK (and not some JRE) ?
>>>>
>>>> Best
>>>> andreas
>>>>
>>>> Ola Spjuth wrote:
>>>>> Hi,
>>>>>
>>>>> After following the docs for jMoby in eclipse (I had to add
>>>>> Home/ to
>>>>> line line 108 in build.xml to look like <fileset
>>>>> dir="${java.home}/../Home/lib">), and generating datatypes, I
>>>>> tried
>>>>> to start dashboard and got the following exception:
>>>>>
>>>>> dashboard:
>>>>> [Dashboard] Exception in thread "main"
>>>>> java.lang.NoClassDefFoundError:
>>>>> org/apache/commons/collections/map/LinkedMap
>>>>> [Dashboard] at
>>>>> org.apache.commons.configuration.BaseConfiguration.<init>
>>>>> (BaseConfiguration.java:54)
>>>>>
>>>>> [Dashboard] at
>>>>> org.apache.commons.configuration.CompositeConfiguration.clear
>>>>> (CompositeConfiguration.java:159)
>>>>>
>>>>> [Dashboard] at
>>>>> org.apache.commons.configuration.CompositeConfiguration.<init>
>>>>> (CompositeConfiguration.java:56)
>>>>>
>>>>> [Dashboard] at
>>>>> org.biomoby.service.dashboard.DashboardConfig.get
>>>>> (DashboardConfig.java:117)
>>>>>
>>>>> [Dashboard] at
>>>>> org.biomoby.service.dashboard.DashboardConfig.getString
>>>>> (DashboardConfig.java:243)
>>>>>
>>>>> [Dashboard] at
>>>>> org.biomoby.service.dashboard.Dashboard.getProperty
>>>>> (Dashboard.java:208)
>>>>> [Dashboard] at
>>>>> org.biomoby.service.dashboard.Dashboard.getComponent
>>>>> (Dashboard.java:485)
>>>>>
>>>>> [Dashboard] at
>>>>> org.biomoby.service.dashboard.Dashboard.<init>(Dashboard.java:176)
>>>>> [Dashboard] at
>>>>> org.biomoby.service.dashboard.Dashboard.main(Dashboard.java:988)
>>>>>
>>>>> I am new to maven and don't really now how I should fix this
>>>>> dependency.
>>>>> Any suggestions for a solution?
>>>>>
>>>>> Cheers,
>>>>>
>>>>> /Ola
>>>>> _______________________________________________
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